4GD3

Structure of E. coli hydrogenase-1 in complex with cytochrome b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the O(2)-Tolerant Membrane-Bound Hydrogenase 1 from Escherichia coli in Complex with Its Cognate Cytochrome b.

Volbeda, A.Darnault, C.Parkin, A.Sargent, F.Armstrong, F.A.Fontecilla-Camps, J.C.

(2013) Structure 21: 184-190

  • DOI: 10.1016/j.str.2012.11.010

  • PubMed Abstract: 
  • We report the 3.3 Å resolution structure of dimeric membrane-bound O(2)-tolerant hydrogenase 1 from Escherichia coli in a 2:1 complex with its physiological partner, cytochrome b. From the short distance between distal [Fe(4)S(4)] clusters, we predic ...

    We report the 3.3 Å resolution structure of dimeric membrane-bound O(2)-tolerant hydrogenase 1 from Escherichia coli in a 2:1 complex with its physiological partner, cytochrome b. From the short distance between distal [Fe(4)S(4)] clusters, we predict rapid transfer of H(2)-derived electrons between hydrogenase heterodimers. Thus, under low O(2) levels, a functional active site in one heterodimer can reductively reactivate its O(2)-exposed counterpart in the other. Hydrogenase 1 is maximally expressed during fermentation, when electron acceptors are scarce. These conditions are achieved in the lower part of the host's intestinal tract when E. coli is soon to be excreted and undergo an anaerobic-to-aerobic metabolic transition. The apparent paradox of having an O(2)-tolerant hydrogenase expressed under anoxia makes sense if the enzyme functions to keep intracellular O(2) levels low by reducing it to water, protecting O(2)-sensitive enzymes during the transition. Cytochrome b's main role may be anchoring the hydrogenase to the membrane.


    Related Citations: 
    • X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli.
      Volbeda, A.,Amara, P.,Darnault, C.,Mouesca, J.M.,Parkin, A.,Roessler, M.M.,Armstrong, F.A.,Fontecilla-Camps, J.C.
      (2012) Proc.Natl.Acad.Sci.USA 109: 5305


    Organizational Affiliation

    Metalloproteins Unit, Institut de Biologie Structurale J.-P. Ebel CEA-CNRS-Université Joseph Fourier, UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-1 small chain
S, T, Q, R
335Escherichia coli (strain K12)Gene Names: hyaA
EC: 1.12.99.6
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
O2-tolerant Hydrogenase-1 in complex with cytochrome b
Find proteins for P69739 (Escherichia coli (strain K12))
Go to UniProtKB:  P69739
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-1 large chain
L, M, J, K
582Escherichia coli (strain K12)Gene Names: hyaB
EC: 1.12.99.6
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
O2-tolerant Hydrogenase-1 in complex with cytochrome b
Find proteins for P0ACD8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACD8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ni/Fe-hydrogenase 1 B-type cytochrome subunit
A, B
235Escherichia coli (strain K12)Gene Names: hyaC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
O2-tolerant Hydrogenase-1 in complex with cytochrome b
Find proteins for P0AAM1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AAM1
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
Q, R, S, T
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FCO
Query on FCO

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Download CCD File 
J, K, L, M
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
J, K, L, M, Q, S
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
F4S
Query on F4S

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Download CCD File 
Q, R, S, T
FE4-S3 CLUSTER
T-CLUSTER
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
J, K, L, M
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
LMT
Query on LMT

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Download CCD File 
A, B, R, T
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
J, K, L, M
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 126.000α = 90.00
b = 165.300β = 90.00
c = 212.800γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2013-01-09
    Type: Database references
  • Version 1.2: 2013-01-30
    Type: Database references